wrProteo: foldChangeArrow2 – R documentation

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foldChangeArrow2

add arrow for Fold-Change to VolcanoPlot or MA-plot

Description

This function allows adding an arrow indicating a fold-change to MA- or Volcano-plots. Optionally the ratio used for plotting can be returned as numeric value. In case of main input as list or MArrayLM-object (as generated from limma), the colum-names of multiple pairwise comparisons can be used for extracting a numeric content which will be used to determine the ratio used for plotting.

Usage

foldChangeArrow2(
  FC,
  useComp = 1,
  isLin = TRUE,
  asX = TRUE,
  col = 2,
  arr = c(0.005, 0.15),
  lwd = NULL,
  addText = c(line = -0.9, cex = 0.7, txt = "expected", loc = "toright"),
  returnRatio = FALSE,
  silent = FALSE,
  callFrom = NULL
)

Arguments

`FC`	(numeric, list or MArrayLM-object) main information for drawing arrow : either numeric value for fold-change/log2-ratio of object to search for colnames of statistical testing for extracting numeric part
`useComp`	(integer) only used in case FC is list or MArrayLM-object an has multiple pairwise-comparisons
`isLin`	(logical) inidicate if `FC` is log2 or not
`asX`	(logical) indicate if arrow should be on x-axis
`col`	(integer or character) custom color
`arr`	(numeric, length=2) start- and end-points of arrow (as relative to entire plot)
`lwd`	(numeric) line-width of arrow
`addText`	(logical or named vector) indicate if text explaining arrow should be displayed, use `TRUE` for default (on top right of plot), or any combination of 'loc','line','cex','side','adj','col','text' (or 'txt') for customizing specific elements
`returnRatio`	(logical) return ratio
`silent`	(logical) suppress messages
`callFrom`	(character) allow easier tracking of message(s) produced

Details

The argument addText also allows specifying a fixed position when using addText=c(loc="bottomleft"), also bottomright, topleft, topright, toleft and toright may be used. In this case the elemts side and adjust will be redefined to accomodate the text in the corner specified.

Ultimately this function will be integated to the package wrGraph.

Value

plots arrow only (and explicative text), if returnRatio=TRUE also returns numeric value for extracted ratio

Examples

plot(rnorm(20,1.5,0.1),1:20)
foldChangeArrow2(FC=1.5)

wrProteo

Proteomics Data Analysis Functions

v1.4.1

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release